Acetylene molecules adsorbed on the Si(001) surface are studied by scanning tunneling microscope and ab initio pseudopotential calculations. In case of room-temperature adsorption, there are basically two different kinds of di-σ bonding geometries at low coverage: (i) on-top and (ii) end-bridge di-σ configurations. The tetra-σ configurations are not found. Theoretical calculations show that the paired end-bridge configuration is dominant at high coverage. Based on these findings, we discuss the results at saturation coverage in the existing literature consistently. Subsequent annealing of the C 2 H 2 /Si(001) surface induces different C-induced surface structures depending on the acetylene coverage. At low coverage, parallel lines of dimer vacancies are observed. As the amount of the adsorbed acetylene increases, the c(4x4) ordered phase replaces the dimer vacancy line phase. Near saturation, clusters are formed and the surface becomes rough.